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Crystal structure of D-Xylose Isomerase in complex with S-1,2-Propandiol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIC PDB entry 1XIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 277 20-28% Propandiol, 0.2M MgCl, 50mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.75 55.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.29 α = 90 b = 99.13 β = 90 c = 102.63 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 2009-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.94 25 93.3 0.049 27.6 5 34311
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.97 88.6 0.4 3.7 5 1509
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R PDB entry 1XIC 1.94 10 34311 32100 3401 97.4 0.1464 0.1464 0.1418 0.1547 0.1816 0.1584 RANDOM
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 3 2889 3355.22
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.059 s_non_zero_chiral_vol 0.042 s_zero_chiral_vol 0.039 s_from_restr_planes 0.0233 s_angle_d 0.023 s_anti_bump_dis_restr 0.012 s_bond_d 0.007 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2998 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 8
Software Software Software Name Purpose SHELXL-97 refinement CNS refinement MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing